Is DSPP p.Ser1172= (c.3516C>T) pathogenic?

DSPP p.Ser1172= (c.3516C>T) is classified Uncertain significance in DSPP (ClinVar, Single submitter, 1 submitter; last evaluated 2016-11-10). Very rare (popmax 0.00362%, sas).

How common is DSPP p.Ser1172= (c.3516C>T) in the general population?

DSPP p.Ser1172= (c.3516C>T) is very rare (popmax 0.00362%, sas) (gnomAD).

DSPP p.Ser1172=

c.3516C>T · rs775371857 · VCV498283

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00362%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -20	GERP -2.4
Overall
CADD	0.673	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00362% South Asian · 3/82,862 alleles

Filtering AF 0.000962% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000467%

Overall 0.000978% 15/1,533,890 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00362%	27,621
African / African-American	0.00293%	34,148
Finnishnot grpmax-eligible	0.00172%	58,202
European (non-Finnish)	0.000789%	126,739

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DSPP
Protein: p.Ser1172=
Coding: c.3516C>T
dbSNP: rs775371857
Type: single nucleotide variant
Location: chr4:87616178 (GRCh38)

Full DSPP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dspp-p-ser1172 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown